1N76 | pdb_00001n76

CRYSTAL STRUCTURE OF HUMAN SEMINAL LACTOFERRIN AT 3.4 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1N76/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2002-11-12 Released: 2003-02-18 
• Deposition Author(s): Kumar, J., Weber, W., Munchau, S., Yadav, S., Singh, S.B., Sarvanan, K., Paramsivam, M., Sharma, S., Kaur, P., Bhushan, A., Srinivasan, A., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of human seminal lactoferrin at 3.4A resolution

Kumar, J., Weber, W., Munchau, S., Yadav, S., Singh, S.B., Sarvanan, K., Paramsivam, M., Sharma, S., Kaur, P., Bhushan, A., Srinivasan, A., Betzel, C., Singh, T.P.

(2003) Indian J Biochem Biophys 40: 14-21

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 76.5 kDa 
• Atom Count: 5,355 
• Modeled Residue Count: 690 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACTOFERRIN	A	690	Homo sapiens	Mutation(s): 0  EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P02788 (Homo sapiens) Explore P02788  Go to UniProtKB:  P02788
PHAROS:  P02788 GTEx:  ENSG00000012223

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO3	E [auth A], F [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.052	α = 90
b = 97.507	β = 90
c = 156.79	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-18 
Deposition Author(s): Kumar, J., Weber, W., Munchau, S., Yadav, S., Singh, S.B., Sarvanan, K., Paramsivam, M., Sharma, S., Kaur, P., Bhushan, A., Srinivasan, A., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2003-02-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary